Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.14.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85304	0.445
27DAP/17DAP	1.23042	0.809
39DAP/27DAP	0.74418	0.353
41DAP/39DAP	1.61521	0.131
42DAP/41DAP	0.83018	1
43DAP/42DAP	1.02861	1
47DAP/43DAP	0.94991	0.815
52DAP/47DAP	0.97035	0.875
57DAP/52DAP	1.00513	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15673	0.029
17DAP/reference	1.29673	0.014
27DAP/reference	1.26958	0.063
39DAP/reference	1.29519	0.083
41DAP/reference	1.59301	0.014
42DAP/reference	1.33361	0.002
43DAP/reference	1.19594	0.095
47DAP/reference	1.26219	0.011
52DAP/reference	1.44174	0.014
57DAP/reference	1.09904	0.952

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88712	0.27
27DAP/17DAP	1.03354	0.942
39DAP/27DAP	1.12259	0.422
41DAP/39DAP	1.13396	0.382
42DAP/41DAP	0.973	0.762
43DAP/42DAP	0.96963	0.774
47DAP/43DAP	1.01388	0.948
52DAP/47DAP	0.99752	0.97
57DAP/52DAP	0.96692	0.665
57DAP/7DAP	0.97554	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85008	0.27
17DAP/reference	0.83487	0.015
27DAP/reference	0.96857	0.215
39DAP/reference	0.77678	0.011
41DAP/reference	0.70981	0.016
42DAP/reference	0.75355	0.01
43DAP/reference	0.75134	0.015
47DAP/reference	0.97206	0.671
52DAP/reference	0.70231	0.026
57DAP/reference	0.67026	0.019

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31957	0.162
17DAP/reference	1.49516	0.12
27DAP/reference	1.38725	0.023
39DAP/reference	1.33282	0.529
41DAP/reference	1.31068	0.019
42DAP/reference	1.45596	0.009
43DAP/reference	1.8368	0.016
47DAP/reference	1.38985	0.015
52DAP/reference	1.29268	0.069
57DAP/reference	1.50685	0.04

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81704	0.041
17DAP/reference	1.17094	0.538
27DAP/reference	0.81126	0.045
39DAP/reference	0.94054	0.36
41DAP/reference	0.97538	0.618
42DAP/reference	1.0462	0.789
43DAP/reference	0.96696	0.523
47DAP/reference	0.93509	0.348
52DAP/reference	1.02702	0.908
57DAP/reference	1.11407	0.636

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23144	0.966
26DAP/20DAP	1.01562	1
34DAP/26DAP	1.03874	1
51DAP/34DAP	0.86199	0.174
52DAP/51DAP	0.98298	1
53DAP/52DAP	1.04262	0.753
55DAP/53DAP	1.10056	0.46
57DAP/55DAP	1.08634	0.898
62DAP/57DAP	0.94936	0.871
68DAP/62DAP	1.08212	1
68DAP/14DAP	0.99979

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89825	0.145

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.77599	0.287
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.47137
Mature Eggplant/Ripe Tomato	0.16396	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89414	0.944
1-1-2/M82	1.0473
12-2/M82	1.27435
12-4/M82	0.99373	1
1-3/M82	N/A	N/A
2-1-1/M82	0.84076
2-1/M82	N/A	N/A
2-6/M82	0.99403
3-2/M82	1.0124
4-1-1/M82	0.9692	1
4-1/M82	0.96794	1
4-3-2/M82	0.85612
4-3/M82	0.82056	0.578
5-3/M82	1.00712	1
6-2/M82	1.07178
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.0191	1
9-3-2/M82	0.99351	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.2139	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.27017	1
IL12-4/WTpooled	1.09931	0.737
IL1-4/WTpooled	0.99932	1
WT/WTpooled	0.87427	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.27693	0.699

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97343	1
DC3000/delta hrp 6h	0.61182
DC3000/delta hrp 12h	1.18219	1
DC3000/delta hrp 24h	1.02838	0.728

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15776	0.11
DC3000 delta B/DC3000 delta AB	1.21755	0.141

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10396	1
Exp 36h	N/A	N/A
Exp 60h	0.9036	0.754

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.03823	1
Var 0h	1.13744	0.374
Var 12h I row2-row1	1.20877	0.324
Var 12h NI row2-row1	0.86305	0.546
Var 36h I row2-row1	1.15068	1
Var 36h NI row2-row1	1.07541	1
Var 60h I row2-row1	1.24539	1
Var 60h NI row2-row1	1.14844	0.904
Time course 0hI-0hNI	1.02997	0.867
Time course 12hI-12hNI	1.01936	0.836
Time course 36hI-36hNI	0.97386	0.533
Time course 60hI-60hNI	1.28164	0.008

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.76059	0.306
transgenic ySAMdc/azygous control (breaker)	0.80988	0.251
transgenic ySAMdc/azygous control (red)	0.94202	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91696	0.062

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.51556	0.277

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.28156	0.105
Manapal/WT (break)	1.15319	1
Manapal/WT (red)	0.61003	0.181